From 6d3138f2985e84bae3fdbea2f13ab27ed9358b9e Mon Sep 17 00:00:00 2001 From: fliem Date: Thu, 25 Oct 2018 21:33:27 +0200 Subject: [PATCH 1/5] added SliceEncodingDirection to stc --- fmriprep/workflows/bold/stc.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/fmriprep/workflows/bold/stc.py b/fmriprep/workflows/bold/stc.py index 697932227..e61a4a398 100644 --- a/fmriprep/workflows/bold/stc.py +++ b/fmriprep/workflows/bold/stc.py @@ -65,12 +65,15 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'): LOGGER.log(25, 'Slice-timing correction will be included.') + # It would be good to fingerprint memory use of afni.TShift slice_timing_correction = pe.Node( afni.TShift(outputtype='NIFTI_GZ', tr='{}s'.format(metadata["RepetitionTime"]), slice_timing=metadata['SliceTiming']), name='slice_timing_correction') + if 'SliceEncodingDirection' in metadata: + slice_timing_correction.inputs.slice_encoding_direction = metadata['SliceEncodingDirection'] copy_xform = pe.Node(CopyXForm(), name='copy_xform', mem_gb=0.1) From f9b2778159c95f7f8ebf103b6d1b4d4e617b9275 Mon Sep 17 00:00:00 2001 From: fliem Date: Thu, 25 Oct 2018 21:35:34 +0200 Subject: [PATCH 2/5] updated zenodo file --- .zenodo.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index b812e9d65..0a6f54c1c 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -78,6 +78,11 @@ "affiliation": "Department of Psychology, Florida International University", "orcid": "0000-0001-9813-3167" }, + { + "name": "Liem, Franz", + "affiliation": "University of Zurich", + "orcid": "0000-0003-0646-4810" + }, { "name": "Poldrack, Russell A.", "affiliation": "Department of Psychology, Stanford University", From f9baab8ffad9d10dfe470a0a2c72b56eef6b6812 Mon Sep 17 00:00:00 2001 From: fliem Date: Thu, 1 Nov 2018 16:22:13 +0100 Subject: [PATCH 3/5] updated reqs to nipype>=1.1.4 --- fmriprep/__about__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fmriprep/__about__.py b/fmriprep/__about__.py index 81590f460..6d6139f18 100644 --- a/fmriprep/__about__.py +++ b/fmriprep/__about__.py @@ -97,7 +97,7 @@ 'grabbit==0.2.3', 'pybids==0.6.5', 'nitime', - 'nipype>=1.1.3', + 'nipype>=1.1.4', 'niworkflows==0.4.4', 'statsmodels', 'seaborn', From 7ed02c99d29d10d52425bd897a51606af4a7de76 Mon Sep 17 00:00:00 2001 From: fliem Date: Thu, 1 Nov 2018 16:23:03 +0100 Subject: [PATCH 4/5] removed empty line --- fmriprep/workflows/bold/stc.py | 1 - 1 file changed, 1 deletion(-) diff --git a/fmriprep/workflows/bold/stc.py b/fmriprep/workflows/bold/stc.py index e61a4a398..d35df7952 100644 --- a/fmriprep/workflows/bold/stc.py +++ b/fmriprep/workflows/bold/stc.py @@ -65,7 +65,6 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'): LOGGER.log(25, 'Slice-timing correction will be included.') - # It would be good to fingerprint memory use of afni.TShift slice_timing_correction = pe.Node( afni.TShift(outputtype='NIFTI_GZ', From ff2796fb49769e35b14e7c0c2411a86c8556be09 Mon Sep 17 00:00:00 2001 From: fliem Date: Thu, 1 Nov 2018 17:09:54 +0100 Subject: [PATCH 5/5] moved slice_encoding_direction input --- fmriprep/workflows/bold/stc.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/fmriprep/workflows/bold/stc.py b/fmriprep/workflows/bold/stc.py index d35df7952..54b44eb52 100644 --- a/fmriprep/workflows/bold/stc.py +++ b/fmriprep/workflows/bold/stc.py @@ -69,10 +69,9 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'): slice_timing_correction = pe.Node( afni.TShift(outputtype='NIFTI_GZ', tr='{}s'.format(metadata["RepetitionTime"]), - slice_timing=metadata['SliceTiming']), + slice_timing=metadata['SliceTiming'], + slice_encoding_direction=metadata.get('SliceEncodingDirection', 'k')), name='slice_timing_correction') - if 'SliceEncodingDirection' in metadata: - slice_timing_correction.inputs.slice_encoding_direction = metadata['SliceEncodingDirection'] copy_xform = pe.Node(CopyXForm(), name='copy_xform', mem_gb=0.1)